Duplication and DNA loss in mitochondrial genome evolution of salamanders

Mitochondria are the site of the citric acid cycle and oxidative phosphorylation (OXPHOS). In animals, the mitochondrial genome is a small, circular molecule averaging 16.5 kb in length. Despite evolutionarily conserved gene content, metazoan mitochondrial genomes show a diversity of gene orders most commonly explained by the duplication-random loss (DRL) model. Despite its apparent role in generating mitochondrial gene order diversity, little is known about the tempo and mode of these events. Here, we determine mitochondrial gene order across the salamander genus Aneides. We then analyze these gene orders in a phylogenetic context to reveal patterns of DNA loss after mitochondrial gene duplication. The evolutionary history of the mitochondrial genome involves massive genomic reduction, where selection for efficiency of mitochondrial replication and transcription has been hypothesized to favor elimination of extra sequence. Our results, however, suggest that there may be no strong disadvantage to extraneous sequences in salamander mitochondrial genomes, although duplicate rRNA genes may be deleterious.